


Second Thoughts

by Folieadeux1013



Category: The X-Files
Genre: F/M
Language: English
Status: In-Progress
Published: 2016-10-27
Updated: 2016-10-27
Packaged: 2018-08-27 10:04:53
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 4
Words: 4,626
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/8397391
Author URL: https://archiveofourown.org/users/Folieadeux1013/pseuds/Folieadeux1013
Summary: Mulder and Scully are on the run when the unthinkable happens. How do they cope when they get their second miracle?





	1. Chapter 1

Mulder stirs as he hears the jingle of keys, and he immediately opens his eyes and shoots up into a seated position, scrambling for his gun on the bedside table.

“Relax,” he hears, and as he comes awake he suddenly recognizes the figure standing before him. Scully is up out of bed and dressed. Mulder still finds it odd to see her dressed so casually, clad in denim jeans, a sandy sweater and grey jacket, despite the fact they’ve been on the run for almost three years now. Some mornings he still expects her to walk out of the motel bathroom as Agent Scully, wearing a polished suit and killer heels. Those days have gone though. Agent Scully has gone. So has her shoulder length red hair – now it’s a mousy brown color, coming to rest midway down her back. Most days – like today – she ties it back, it’s practical that way, but others she lets it curl naturally. She hates it, and Mulder must admit he misses her red locks, but it has to done. She disappears into the crowd as a brunette. It’s yet another price she’s having to pay for following him on the run.

“Scul –”

“Sarah,” she interrupts, warning him. Scully doesn’t look impressed, whether it’s because of the use of her real name or the fact that he’s awake Mulder doesn’t know. 

“Sarah.” The name still feels foreign on his tongue, as does his own alias, Ben. It was Scully’s turn to choose this time, and she opted for traditional names. But old habits die hard, and every now and then one of them – or sometimes both – will slip up, and their old names will roll off the tongue. And of course there are quieter, more intimate moments, when anything other than ‘Dana’ or ‘Scully’ just won’t do. 

“Go back to sleep,” Scully says, whilst slipping the car keys into her jacket pocket. Mulder blinks up at her sleepily. 

“Where are you going?”

“Just out,” she replies dismissively, while Mulder narrows his eyes. 

“Just out?” He smiles. “You’re not trying to walk out on me are you?” As soon as he says the words his smile fades, and he almost dreads her reply. It could happen. Personally he’s not sure why she’s followed him this far either, especially after all she’d been through and all she’d had to sacrifice. Life on the road was hardly easy, and yet still she stayed.

“Don’t be ridiculous Ben. I need to go to the grocery store.”

Mulder scratches his head. There’s something she’s not telling him, and he’s not about to give up until he gets it from her. “Are we out of things already? We only went on Tuesday.” Their store trips are carefully planned. Always at the busiest time of day – that way people are rushing around too much to spot them, and they blend in easier on CCTV. And they never go alone, just in case they have to keep running. 

Scully moves to speak but instead changes her mind and nods. A frown forms on her face as she watches Mulder shift to get out of bed. “What are you doing?”

Scratching his belly, Mulder gets to his feet and pads over to the chair, grabbing the jeans he discarded the night before. “I’m coming with you,” he says to her through a yawn as he slips on his pants.

“It’s fine, I can go alone.”

“No you can’t S…Sarah. What if something happens?”

“I’ll be quick. Nothing’s going to happen.”

“That’s what they say in horror movies right before something happens.”

“This isn’t a horror movie Ben,” she replies tersely. It might not be a horror movie, but often it’s like they’re living in a nightmare that they’re unable to wake from. “It’s a quick trip to a grocery store.”

“Why can’t it wait?” Mulder asks, ignoring her wish for him to stay at the motel. He finds a fresh t-shirt and slips into it. “I thought we’d got everything.”

“We did, but I just remembered something else.”

“What?” As Mulder finishes dressing, he turns to face his partner, noticing her unwillingness to meet his eye. “What is it?” She says nothing, instead folding her arms in front of her. Suddenly he’s not entirely sure that she’s not leaving him. “Dana?” he whispers, nausea creeping in. He wants her to answer him, but yet he doesn’t; scared of what she’s about to say. He’s known it, deep down, ever since they went on the run. She needs to be back home with her family, in a job she loves, living a normal life. Running from town to town, staying in crappy motels and eating out of tin cans isn’t what she deserves. 

“I didn’t mean to wake you,” Scully says in a small voice, swallowing hard. “I was just going to go –” 

“Go…” Mulder repeats, letting the words sink in. She was just going to leave.

She shakes her head. “It’s not what you think.”

“Oh really? So this isn’t it then? You’re not walking out?”

“I’m…what? No!” Scully exclaims, and Mulder instantly breathes a sigh of relief. She’s not leaving him. She really is just popping out. 

“You’re not?” A shake of the head. “Then why the sneaking around? And why are you going to the grocery store?”

“I just need some bread.”

“Bread.” She’s lying and they both know it.

“Drop it Mulder.” She doesn’t even lower her voice, and neither of them notice that she’s used his real name.

“Not until you tell me what you’re up to.”

“Please.”

“Tell me. I don’t get why you won’t tell me. I mean it’s not like it’s my birthday and you’re planning a surprise. Are you sick? Because if you are we can get you some help and –”

“I’m pregnant,” Scully suddenly snaps, stopping Mulder in his tracks. He feels the room start to spin and his legs buckle as he registers her words. 

“You’re…what?”

“I’m…I think I’m…I think I’m pregnant.” Scully’s eyes fill with tears, and a lump forms in Mulder’s throat too. 

“How…?” He immediately regrets the question. He knows how. They’ve been trying to be careful since they’ve been on the run for a number of reasons. For starters, a baby isn’t practical if you’re a wanted man, and then of course there’s William… They always knew that there was a risk Scully could fall pregnant again – after all, it had happened once – but they certainly didn’t think it would ever happen. “I mean…I know how,” he continues. “But…are you sure?”

“I’m about 80 percent sure,” Scully admits.

“So there’s still a chance…?”

“I’m late.” Scully is never late, her period arriving each month like clockwork. “And the signs are there. Nausea, dizziness…”

“But you never said…”

“I thought it might be the stress of everything.”

Suddenly Mulder feels lighter. “It could be stress,” he agrees, but Scully shakes her head. She doesn’t think it is. 

“I want to do a pregnancy test,” she announces, and Mulder nods. “I need to know.” She sniffs, wiping her eyes. 

“Of course. And if it’s positive…?”

“I can’t think about that now,” she answers quickly. “I can’t believe this is happening.”

“I’m sorry.” He feels helpless, helpless and sick. All he can think about is the tiny little boy he kissed goodbye three years ago. They can’t go through that again. If Scully is pregnant, things will change. She’ll have to leave him of course, and go back to her life in DC. She’ll need healthcare and a proper roof over her head. He wants nothing more than to go with her, but Mulder would rather his child think of him dead than a murderer. And right now he can’t think of his child, because it’ll be a child he’ll never meet. He’s going to be sick. 

He watches as Scully heads to the door and suddenly springs back into action, stopping to step into his sneakers, before joining her at the door. 

“Scully?” 

She pauses and looks up at him, her expression fearful. They’re both scared, about what’s happening and what the future holds – especially now. “Whatever happens we’ll deal with it. We’ll be ok. All of us.” 

Scully says nothing, but reaches out and squeezes his hand. Without letting go, she leads him out of their motel room and towards the car, the two of them ready to discover their fate.


	2. Chapter 2

They rush to the store to buy a pregnancy test, and end up leaving with three. Mulder wanted to buy more – “best of five,” he’d quipped, with a false smile and fear in his heart - but no, three it was. As the store worker grinned and wished them luck, the two of them swallowed their tears and politely said thanks, before leaving and returning to the motel in double quick time. 

As soon as they arrive back Scully disappears into the bathroom, closing the door firmly behind her, her meaning loud and clear. She’s doing this alone. Again.

So Mulder sits on the edge of the too-soft mattress, bouncing his leg nervously while he waits; his eyes trained on the clock on the TV. He forgot to ask Scully how long it will take – he’s pretty sure he’s seen commercials for tests that take just a minute or so and so he starts to count to himself, “one Mississippi, two Mississippi…” right up to sixty and then he pauses, listening out for signs of movement in the bathroom. When he doesn’t hear anything he starts again, repeating the process, until he realizes that ten minutes have now passed. Surely no test takes ten minutes, he thinks to himself, and so he gets to his feet and pads over to the bathroom. There’s no sound coming from within and so he taps on the door softly. “Sarah?” Nothing. He taps again and when further knocks are greeted with silence he tries the handle. The door is locked. “Sarah?”

He’s worried now, half wondering whether she’s escaped out of the bathroom window. It’s a small opening, but Scully is pretty tiny herself, and right now there’s barely anything on her. Come to think of it, in recent days her appetite has all but disappeared. Now he knows why – or at least he’s 80 percent sure. “Scully? Scully let me in. Scully!” He doesn’t care that he’s shouting her real name; that anyone could hear and their charade could be discovered. Right now all he cares about is his partner on the other side of the door, and what she must be going through. 

He’s considering kicking down the door when it suddenly opens and he comes face to face with Scully. “What -?” He hesitates as he registers the tears in her eyes, but before he can say anything else she pushes past him and heads towards the bed. He’s distracted momentarily by the sight of the three tests resting on the edge of the sink, and he edges closer, unsure whether Scully’s tears are because the results are positive or negative. He leans over, his eyes registering the lines, and he immediately turns and follows Scully out into the bedroom. 

She’s hiding underneath the covers now, wisps of her hair barely visible above the comforter. Mulder is by her side in seconds, crawling onto the bed and wrapping his arm around her, pulling his blanket-covered partner in towards him. She gravitates into his arms but doesn’t surface, unwilling to meet his eye, and so Mulder simply holds her as she sobs. “I’m sorry,” he whispers, pressing his lips against the comforter. There’s a range of emotions shooting through him right now, and he feels like crying too. 

The tests are all positive. Scully is pregnant. Once again life has dealt them a cruel blow. They should be happy about this – after all, Scully is supposed to be barren, and here she is, pregnant for the second time against all odds. But Mulder knows that they’re both thinking about another baby, an impossibly tiny baby boy with Scully’s eyes and coloring, and his own lips and chin. The perfect combination of them both who they may never know, who’s now potentially hundreds of miles away, calling two other people ‘mom’ and ‘dad’. 

He knows they have big decisions ahead of them - after all they weren’t expecting this. Scully can’t remain on the run while she’s pregnant – she’ll need hospital care very soon. But Mulder isn’t sure he can let her go, or more importantly let her go through all of this alone. He missed out last time with William, and he doesn’t think he can stand to miss out again. This baby could be his chance to do the right thing this time and to make amends. But as he holds Scully, and listens to her heartbreaking sobs, sobs which are cutting through him like a knife, suddenly he’s not even sure there is going to be a baby. Scully might decide that she can’t go through it all again, memories of William too painful to bear. They’ve got a lot to talk about, Mulder muses, but right now Scully is in no fit state to do so. So instead he settles his head on the pillow and holds his partner while she cries, and soon his own tears begin to fall.


	3. Chapter 3

They spend the rest of the morning, crying and sleeping, and crying some more, trying to take in the news. When Mulder opens his eyes at one point, he sees that Scully has now surfaced from beneath the comforter, and is looking back at him, her eyes watery. She looks exhausted, exhausted and heartbroken.

“Hey,” he says, reaching out to brush a strand of hair out of her eye. “How are you doing?” It’s a stupid question really, he thinks to himself. He knows how she’s doing. Badly. She’s in shock – they both are, and they’re both trying to take it all in. It’s supposed to be a happy time for them both – after all it’s a baby, a new addition to their family - but it’s turning out to be anything but.

Scully closes her eyes and speaks, her voice unsteady. “Mulder,” she begins. “I don’t know if I can do this.” She releases a shaky breath. “I don’t know what to do. I don’t know if I can do this.” 

Mulder nods. He was expecting her to say that, but the words still make his heart hurt. 

“I just want William back,” she continues, the tears falling once more. Mulder isn’t sure if she has many more tears left to cry. 

“I know,” he replies, kissing her warm forehead. “I do too.” He sighs heavily, feeling so guilty, guilty at the situation, the two of them on the run; and guilty for getting her pregnant, guilty for leaving her in the first place. 

“There’s a part of me that thinks this is some kind of punishment for giving William away.”

“It’s not a punishment Scully,” Mulder insists. “It’s a baby, not a punishment. But I know what you mean,” he adds. 

“What are we going to do?”

That’s the big question, and Mulder doesn’t know how to answer. “Well,” he begins. “I guess there are a few options.” He hesitates, swallowing hard. “If you want to have this baby, we can contact Skinner and see if he can get you into a hospital. It might be safe for you to go as yourself now, as long as I’m not with you. I mean I’m sure your mom would let you stay with her, especially if she knows that you’re back for good and away from me. Or –”

“I’m not leaving you Mulder.” Scully opens her eyes and gives him her best glare. She’s deadly serious. 

He smiles. “The way I see it Scully, you’re going to have to. If we decide not to go through with it…” He swallows. It’s painful to think about, even though it is an option for them. “You’ll need hospital treatment, and if…well if you change your mind, you can’t have a baby while we’re running from motel to motel. It’s not safe, and it’s certainly not a good start to their life.”

“I know,” Scully says, sniffing. “I don’t know what do to.”

Mulder doesn’t either. “How many weeks do you think you are?”

“Six, or thereabouts,” Scully answers. 

“Ok, so we don’t have to make a decision right now, do we?” 

Scully shakes her head. She looks as though she’s going to say something, but then she stops herself. “No.”

“We can take some time and think about this and what we’re going to do.”

“What do you think about this?”

“I think…” He starts again. “I really don’t know, other than the fact I’m completely stunned.” Scully huffs a laugh, and he knows she’s feeling exactly the same. 

“On the one hand it’s like a kick in the teeth in a way. I feel numb and I just…I feel a little stupid that I didn’t think this would ever happen. But then…then I keep thinking about William and the last time I held him. How tiny he was and how he looked in my arms. I think about the day we brought him home to your apartment and spent the whole night in bed just looking at him, counting all of his fingers and toes and watching every move he made. I keep thinking about him growing up and all of the things that we’ve missed along the way. And I know that our situation is far from ideal, but there’s a part of me that thinks we could do this Scully. That maybe this baby is just what we need.” He shrugs. “But I would never tell you what to do. I know that having a baby isn’t only crazy, but it will bring up a range of emotions too. It’ll be painful and hurt and it’s going to bring back memories of William but…”

“But at the end of the day it’s our baby,” Scully finishes and Mulder nods. 

“Yes.”

“I can’t give this baby away,” she announces. “I can’t go through that again.”

“Scully.” Reaching out, Mulder takes hold of her hand. “You did what any good mom would have done in the circumstances. You protected our son by doing what was best.” Scully nods but Mulder knows that she will always blame herself for putting William up for adoption, and nothing will ever change that. Out of the corner of his eye he sees Scully’s other hand slide down and curl protectively over her stomach. The move brings a tear to his eye. There’s a little person growing inside of her. 

“Mulder?”

“Yeah?”

“I think I want to have this baby.”

He pauses in shock – after all, a few minutes ago she wasn’t sure what she wanted to do. Then, after a moment, a smile forms on his face. “Ok.”

“I know it’s going to be tough and I’m not getting any younger and that we’re insane for even thinking about doing this...”

Mulder’s smile widens. “When has that ever stopped us?”

“Does this mean you’re ok with it? If that’s what I decide to do.”

“I want what you want,” he replies. “It’s going to be tough if you want me to be there.”

“I do. That’s if…” she gives him a questioning look and he nods.

“Of course I do. I don’t know how we’re going to do it, but I know I want to be there for you.” His hand moves to cover hers on her stomach. “We can do this.”

“Really?”

“Really.” He doesn’t admit that he’s absolutely terrified, both at the thought of having a baby and the fear of them getting found out, not when she’s looking at him with such love and hope in her eyes. He can worry later. Instead he leans over and kisses Scully squarely on the lips. Whatever happens, they’ll deal with it. 

Together.


	4. Chapter 4

Mulder looks up as he hears the door to the diner open, and he bites back a smile as Walter Skinner steps into view. His former boss is trying to blend in as a civilian, his formal suit of days gone by replaced with jeans and a dark plaid shirt. All he needs is the cowboy hat to go with it, thinks Mulder, but he says nothing, instead nodding as Skinner approaches the booth where he and Scully are sat. The diner is busy but not crowded, the people at the other booths are too distracted to notice Skinner’s arrival, and the music sounding out of the jukebox is loud enough to soak up any private conversations. 

Scully sits perfectly still opposite Mulder, sipping at her soda in a bit to keep the nausea at bay. Her morning sickness began just a few days ago and seems to be hitting her hard. She’s vomiting regularly each day like clockwork, and when she’s not being physically sick, she’s experiencing feelings of nausea and dizzy spells. Because of this, they’ve remained in one place for the past week – Cheyenne, Wyoming – so that Scully can rest and get her strength back. They both know they’ll have to move on soon – especially if Skinner has been followed – but hopefully he’ll help to clear their path ahead. Now all they have to do is ask him. 

“You look like shit, the pair of you,” Skinner says in greeting as he slips into the booth next to Scully. He doesn’t sound particularly amused, no doubt pissed at having to fly across the country to find them, but Mulder can hear an element of concern in his voice too. He knows they wouldn’t contact him without good reason, and after three years on the run, they finally have reason. 

“Thanks for coming Walter,” Scully says softly with gratitude in her eyes as she looks at her former boss. “It’s good to see you again.”

Skinner has aged since they last saw him. He looks tired and worn, dark circles beneath his eyes, but he’s still the same Skinner, unamused but dependable. Scully moves to pour him a glass of water from the jug sitting in the middle of the table but stops herself, the movement too much for her. Coming to her assistance Mulder takes over, then slides the glass over to the man opposite him. Skinner nods in thanks. 

“How was your journey?” Mulder asks as a waitress passes them. To anyone passing it sounds like a simple, polite enquiry, but Skinner understands the meaning behind the questions.

“I wasn’t followed,” Skinner murmurs. “I covered my tracks and booked a ticket to Vegas too.”

Mulder snorts. “We appreciate you giving up the slot machines to come here.”

Skinner doesn’t smile back. “Alright, enough of the niceties, what’s going on?” He glances back and forth between Mulder and Scully. “There must be some reason you called me all of this way. “What’s -?”

“Excuse me.” Pressing her fingers to her lips, Scully gestures for Skinner to let her out of the booth. Confused, he does so, then looks on as she walks swiftly in the direction of the ladies’ bathroom. Mulder grimaces, feeling bad for his partner. Scully is sensitive to smell, and the diner is hardly the best environment for her. 

Confused, Skinner sits back down. “Is she alright?”

Mulder opens his mouth to speak but is interrupted by the waitress seeking Skinner’s order. Unamused at being interrupted, he snatches up a menu from the table, scans it at speed and orders an omelette, waiting for the waitress to walk out of earshot before he tries again. “What’s –” He pauses as he sees Scully exit the bathroom and move to walk back towards them. He watches as she suddenly hesitates, turns on her heel and heads back to the bathroom, his eyes narrowing. “Alright, what’s going on. Is she ok?” Mulder says nothing, his expression giving his answer away. “Is she sick? She’s sick,” Skinner says, answering his own question. “Is it the cancer?” He sighs. “Tell me it’s not the cancer.”

“It’s not the cancer,” Mulder answers, watching his former boss relax. “But, it’s complicated.”

“Define complicated.”

“She’s pregnant.”

Mulder’s words are greeted with silence as Skinner absorbs the information. After a moment the other man’s face darkens, and he shakes his head. “Are you two completely stupid?”

“It wasn’t planned.”

“I should hope not.” He sighs again. “And that’s why you need my help.”

“She’ll need hospital treatment.”

“Right.” Skinner clearly hasn’t understood. 

“Scully wants to have the baby,” Mulder informs him, and clearly that’s not the answer Skinner is expecting. 

“She…What?” He rubs his eyes wearily, the events of the past 24 hours catching up with him. “How the hell do you two plan to live a life like this with a newborn?”

“I know.”

“It’s not safe.”

“I know that too. But she wants to go through with the birth, and there’s no way she’d even consider giving the baby away. Not after last time.”

“No,” Skinner says in agreement, softening as he remembers that awful time. “I can’t imagine she does.”

“Putting William up for adoption almost broke her.” Reaching out, Mulder lifts his own glass of water and takes a sip. “We know it’s crazy and that there are many many risks involved, but it’s what we’ve decided. Scully wants this. She deserves this.”

Skinner nods, just as Scully emerges from the bathroom once again. This time she makes it all the way back to their booth, choosing to sit next to Mulder instead. 

“I umm…I hear congratulations are in order,” Skinner murmurs, watching Scully shift awkwardly in her seat. She focuses on Mulder’s glass of water, unable to meet his eye. “The circumstances aren’t ideal,” she admits softly. Mulder startles as he feels her hand take hold of his beneath the table. He knows she’s scared, and they both know that Skinner is their only hope. Without him they’ll have to go it alone. 

“No.”

“But we want this,” Mulder adds firmly, and Scully nods in agreement. 

“Sir…” The word feels foreign on her tongue. “I know we’re asking a lot, and there’s a lot at risk here, but we really need your help. I need to see a doctor, and pretty soon we’re going to have to stop running. We need a base, new permanent identities.”

“You know that I can pave the way for you to come back to DC don’t you?” 

Scully nods. “I do, but I’m not going back alone.”

Mulder squeezes her hand, but he can’t help but feel guilty. If it wasn’t for him she could go back to her mom and get her life back, but he knows she won’t. 

“Alright.” Skinner isn’t exactly surprised at her words.

“Does that mean you’ll help?”

“Of course I’ll help,” he says, as if there was never any doubt. “I wouldn’t be here if I wasn’t prepared to help.”

“Thank you.”

“I’ll go back and make some enquiries.” 

“We appreciate it,” says Mulder, as Scully lets go of his hand and shifts in her seat. “More than you’ll ever know.”

“Excuse me.” She doesn’t wait for a response before she’s rushing back towards the bathroom, passing the waitress who’s on her way with their food. Skinner waits until she’s set it all down on their table before he speaks again. “If you screw this up –”

“I won’t,” Mulder promises. “It’s going to be different this time. I’m different this time.”

“Because I swear to God –”

“I know sir, I know. I’m going to do everything I can to protect her. Both of them.”

After a moment Skinner relaxes. He believes it too.


End file.
